My issue with the ship scales for JJ's reboot is that the ships seem too big. A super-ship for no reason just seems dumb.
If Starfleet was planning to go to war larger ships would be a necessity to carry troops and supplies. A ship like the Vengeance
would be very useful under that type of scenario. It seems that the Abramsverse doesn't work under the assumption that two ships are going to sit and slug it out and that you can hold a planet with twenty people. Wars are likely to be much more like the real thing.
These ships are grains of sand on a beach compared to the size of a star system. I don't think the larger sizes really constitutes an issue except for those who are locked in on how big ships should be based on the prior series/movies.